Google Backs Harvard Scientist's 100,000-Genome Quest. (Bloomberg, Feb 2008, John Lauerman) ; HMS Prof To Expand Genome Database (Crimson, Mar 2008, June Wu). "plans to spend $1 billion" Comment: I'm not sure where they got that number -- possibly multiplying the 100,000 volunteer genomes (mentioned in our latest IRB update) by the X-prize goal of $10K per genome. The PGP goal is closer to $1K (for a partial genome + transcriptome). More importantly, our goal is to make the cost of genomic data and trait data low enough so that large numbers of genetically-literate consumers would have such data anyway and could donate at close to zero cost.
Celebrity genomes alarm researchers (Nature, May 2007, Erika Check) Acknowledging the role wealthy early-adopters play in new technologies and the edutainment value of celebrity, we appreciate Ericka Check's story, yet note the need to clarify the Personal Genome Project stance on elitism and celebrity. We have pursued a 30 year long effort to get the cost of genomics down to an affordable $1000, even sacrificing part of our early role in the genome project, feeling it too expensive ($3 billion) relative to developing technology suitable for average citizens. The PGP was designed in consultation with ethicists to be scaleable (via pre-consent educational tools) to a diverse 100K to million participants, minimizing risk at each stage. The Harvard IRB requested solid knowledge of genetics and risks among the volunteers, which so far consist of educators and stakeholders in public genetics issues (not wealthy celebrities). We ask potential PGP volunteers to consult their families, and this has resulted in exclusion of PGP volunteers. PGP data while obtained with consent to full disclosure, are intended to be initially more secure than feasible with a 'public researcher-only' database, so that subjects can intelligently decide to opt-out before a broad set of researchers (including potentially careless ones) gain access. We are concerned that current practice does not educate subjects about the various means of re-identification from detailed genome/phenome datasets (arep.med.harvard.edu/PGP/Anon.htm). The prospect of a poorly-handled re-identification 'event' strikes us as a potentially larger set-back to genomics than a perceived delay in getting a large set of research subjects.
Reading the Book of Jim. .. pioneering the 'personal genome.'
(Newsweek, June 2007, Sharon Begley).
"Genetic variations linked to disease are sprinkled across 0.01 percent of the genome, estimates George Church of Harvard University, who has been pushing technology to make genome sequencing affordable. Those regions could be sequenced for $1,000, he estimates, "and would give you 95 percent of the heavy-hitting mutations"
Comment: While 0.01% is a whopping 300,000 positions and those could cover 95% of the 'heaviest' mutations, the PGP is aiming at 100 times that amount (i.e. a $1K 1% genome) initially and hope to improve on that soon.
Church Hopes to Make DNA Decoding Accessible (Crimson, Aug 2006, Katherine Gray)
"The method he devised is still the most common way people look at three dimensional structures"
Comment: The basic idea had existed already since the mid '60s. Perhaps I was one of the first to make it computational, but that is not important.
Another bit of software that I did as part of a team called CORELS has been kept alive now for 30 years by Joel Sussman is arguably more significant. That's a long time for software to survive.
"Their DNA has already been partially sequenced"
Comment: Only two of the ten subjects have been through the consenting and blood-letting (see Globe article below), and only one of those has any polony genome sequencing so far.
We have just begun actively recruiting volunteers for the remaining slots. Women in general and men with non-european ancestry are especially encouraged to apply (see PGP).
"An expert examining himself is going to be much more effective"
Comment: An expert examining himself or herself might be more effective for some things, but biased for other things, and generally less effective than a team of experts.
--George
Scan Artist (Boston Globe, Jul 2006, Michael Fitzgerald)
"George and I are co-principal investgiators of the Personal Genome Project [PGP]. George, of course, is an exhibitionist. So what he said is, in the interest of really exploring this issue, he's putting his phenotype, his genotype, and everything on the Web. And I, as co-PI, have said I am also willing to contribute my genotype to research. That was a much more challenging conversation with my wife and daughter. The RFID really has no implications for them other than that my whereabouts could conceivably be tracked. The PGP has a lot of privacy implications."
Comment: John told me that this quote didn't capture his meaning, but even if a a bit off-target, it still has value in generating interesting discussion.
The HMS IRB requested that I participate in the PGP, and like most of their suggestions this turned out to be very helpful.
The PGP is much more 'private' than initially concieved. 'Exhibitionist' has a ring of 'in-your-face behaviorial pathology', while one would hope that the intent of all ten PGP subjects is more a 'willingness to share' (as privately as possible) and to be part of a research team.
In a very important sense, PGP is more private than nearly all medical research today, wherein the subjects are kept in the dark, and hence have little basis on which they can decide to opt-out of a project, and conversely no option to shine light on it by making it public either.
(See the above Crimson article and also the discussion of problems with current anonymity promises.
--George